def drop(configpath, mysqlcfg, verbose, debug):
"""drop databases from a MySQL server"""
mysql_info = read_mysql_config(mysqlcfg, "mysql")
account = HostAccount(
mysql_info["host"],
mysql_info["user"],
mysql_info["passwd"],
port=mysql_info["port"],
)
server = DbConnection(account, db_name="PARENT", pool_recycle=36000)
cursor = server.cursor()
release, remote_path, local_path, species_dbs = read_config(configpath)
content = get_db_name(account=account, release=str(release))
content = [str(n) for n in content]
dbnames = reduce_dirnames(content, species_dbs)
click.echo("The following databases will be deleted:")
click.echo("\n".join(" %s" % d for d in dbnames))
try:
click.confirm("Confirm you want to delete the databases", abort=True)
except click.exceptions.Abort:
click.echo("EXITING")
exit(0)
for dbname in dbnames:
click.echo(f"Dropping {dbname}")
_drop_db(cursor, dbname)
if verbose:
display_dbs(cursor, release)
cursor.close()
def test_get_all_available(self):
"""should return a listing of all the available databases on the
indicated server"""
available = get_db_name()
# make sure we have a compara db present -- a crude check on
# correctness
one_valid = False
for db in available:
if db.type == "compara":
one_valid = True
break
self.assertEqual(one_valid, True)
# now check that when we request available under a specific version
# that we only receive valid ones back
available = get_db_name(release="46")
for db in available:
self.assertEqual(db.release, "46")
def display_available_dbs(account, release=None):
"""displays the available Ensembl databases at the nominated host"""
db_list = get_db_name(account=account, db_type="core", release=release)
db_list += get_db_name(account=account, db_type="compara", release=release)
rows = []
for db_name in db_list:
species_name = db_name.species
if species_name:
common_name = Species.get_common_name(db_name.species, level="ignore")
if "compara" in db_name.name:
species_name = common_name = "-"
rows.append([db_name.release, db_name.name, species_name, common_name])
table = make_table(
header=["Release", "Db Name", "Species", "Common Name"], data=rows, space=2
)
table = table.sorted(["Release", "Db Name"])
table.legend = (
"Values of 'None' indicate cogent does not have a value for that database name."
)
return table
def test_getdb(self):
"""should discover human entries correctly"""
for name, db_name in [
("human", "homo_sapiens_core_49_36k"),
("mouse", "mus_musculus_core_49_37b"),
("rat", "rattus_norvegicus_core_49_34s"),
("platypus", "ornithorhynchus_anatinus_core_49_1f"),
]:
result = get_db_name(species=name, db_type="core", release="49")
self.assertEqual(len(result), 1)
result = result[0]
self.assertEqual(result.name, db_name)
self.assertEqual(result.release, "49")
def show(release, mysqlcfg):
"""shows databases corresponding to release"""
if mysqlcfg.name == _mycfg:
click.secho(f"{show.help}\n")
click.secho("use --help for more options")
exit()
mysql_info = read_mysql_config(mysqlcfg, "mysql")
account = HostAccount(
mysql_info["host"],
mysql_info["user"],
mysql_info["passwd"],
port=mysql_info["port"],
)
names = get_db_name(account=account, release=str(release))
click.echo(f"Databases at host='{account.host}' for release={release}")
if names:
click.echo("\n".join(" %s" % n for n in names))
else:
click.echo(" None")